During the simulation of protein with Fe (II) ligating
with 2 His and 1
Asp residues at active site, I set every thing right
including Kb value
but failed to deprotonate NE2 atoms of 2 His residues
ligating that
Fe(II).
What do you mean by failed ? This should not be a problem.
You can choose the protonation state of a his ... check
the ffXXX.rtp file.
After 2ns simulation run, the average pdb
structure shows that
the flip of His ring out from Fe (II), but the
Asp-oxygen moved much
closer to Fe (II) than its original position. If I
compute RMSF for Fe
(II), showing value of "0" through out the simulation
run. The RMSF "0"
indicates Fe (II) originally retained in its position,
0 fluctuations at all !!! You fixed its position or
something ? That does not seems right !!
but the ligating
His flipped and Asp as a single residue held the Fe (II)
at its original
position. So now please tell me whether this simulation
is valid?
The simulation that you discribe does not seem to be
a good representation of your system ...
XAvier
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